Projects:RegistrationLibrary:RegLib C35 - Revision history

Grundlett: Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

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Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

Meier: /* Modules */

2011-03-01T18:28:31Z

Modules

Meier: /* Key Strategies */

2011-03-01T18:27:28Z

Key Strategies

Meier: /* Download */

2011-03-01T16:15:54Z

Download

Meier: /* Registration Challenges */

2011-03-01T16:13:42Z

Registration Challenges

Meier at 16:13, 1 March 2011

2011-03-01T16:13:27Z

Meier at 16:10, 1 March 2011

2011-03-01T16:10:33Z

Meier at 16:09, 1 March 2011

2011-03-01T16:09:56Z

Meier: /* Registration Results */

2011-03-01T16:07:45Z

Registration Results

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= v3.6.1 [[Image:Slicer3-6Announcement-v1.png‎|150px]] Slicer Registration Library Case #35: Mouse Colon Brain MRI =
=== Input ===
{| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
|[[Image:RegLib_C35_Thumb1.png|150px|lleft|case A]]
|[[Image:RegArrow_NonRigid.png|100px|lleft]]
|[[Image:RegLib_C35_Thumb2.png|150px|lleft|case B]]
|-
|fixed image 1/target MRI mouse 1
|
|moving image MRI mouse 2
|}

=== Modules ===
*'''Slicer 3.6.1 recommended modules:''' [http://www.slicer.org/slicerWiki/index.php/Modules:SurfaceRegistration '''SurfaceRegistration'''], [http://www.slicer.org/slicerWiki/index.php/Modules:Transforms '''Transforms (manual registration)'''], [http://www.slicer.org/slicerWiki/index.php/Modules:FastMarchingSegmentation-Documentation-3.6 '''Fast Marching Segmentation'''], [http://www.slicer.org/slicerWiki/index.php/Modules:HistogramMatching-Documentation-3.6 '''Histogram Matching'''], [http://www.slicer.org/slicerWiki/index.php/Modules:ModelMaker-Documentation-3.6 '''Model Maker'''],

===Objective / Background ===
Aim is to register the two MRIs such that the colon aligns.
=== Download ===
*DATA
**[[Media:RegLib_C35_Data.zip‎|'''Registration Library Case 35 ''' (Data, zip file 46 MB) ]]
*See detailed pipeline with parameter settings below

=== Keywords ===
MRI, colon, mouse, masking, non-human, non-rigid,manual, unsolved

===Input Data===
*reference/fixed MRI: 0.12 x 0.12 x 0.1 mm, 512 x 512 x 94
*moving MRI: 0.09 x 0.09 x 0.1 mm, 512 x 512 x 94

===Registration Challenges===
*The image content to be registered is less than 10% of the total image and of low energy (close to background);
*there's large portions of the colon for which no matching/corresponding structures exist, i.e. a straightforward one-one mapping is not avail.
*other landmarks (kidneys etc.) are very different in position and size

===Key Strategies===
*This is a '''challenge case''' and currently unsolved. Best hopes are combinations of manual, fiducial and surface-based registration
*'''Slicer 3.6.1 recommended modules:
** [http://www.slicer.org/slicerWiki/index.php/Modules:SurfaceRegistration Surface Registration]
** Plastimatch

=== Registration Results===
[[Image:RegLib_C35_Model.png |200px| very rough surface models of colon help visualize misalignment] very rough surface models of colon help visualize misalignment 
[[Image:RegLib_C35_unreg.gif‎ |500px|original unregistered]] original, not registered 
[[Image:RegLib_C35_reg.gif |500px| after surface registration (rigid) + manual correction]] after surface registration (rigid) + manual correction

@@ Line 16: / Line 16: @@
 === Modules ===
-*'''Slicer 3.6.1 recommended modules:'''  [http://www.slicer.org/slicerWiki/index.php/Modules:PythonSurfaceICPRegistration-Documentation-3.6 '''SurfaceRegistration'''],    [http://www.slicer.org/slicerWiki/index.php/Modules:Transforms '''Transforms (manual registration)'''],  [http://www.slicer.org/slicerWiki/index.php/Modules:FastMarchingSegmentation-Documentation-3.6 '''Fast Marching Segmentation'''],   [http://www.slicer.org/slicerWiki/index.php/Modules:HistogramMatching-Documentation-3.6 '''Histogram Matching'''],  [http://www.slicer.org/slicerWiki/index.php/Modules:ModelMaker-Documentation-3.6 '''Model Maker'''],
+*'''Slicer 3.6.1 recommended modules:'''  [https://www.slicer.org/wiki/Modules:PythonSurfaceICPRegistration-Documentation-3.6 '''SurfaceRegistration'''],    [https://www.slicer.org/wiki/Modules:Transforms '''Transforms (manual registration)'''],  [https://www.slicer.org/wiki/Modules:FastMarchingSegmentation-Documentation-3.6 '''Fast Marching Segmentation'''],   [https://www.slicer.org/wiki/Modules:HistogramMatching-Documentation-3.6 '''Histogram Matching'''],  [https://www.slicer.org/wiki/Modules:ModelMaker-Documentation-3.6 '''Model Maker'''],
 ===Objective / Background ===
@@ Line 40: / Line 40: @@
 *This is a '''challenge case''' and currently unsolved. Best hopes are combinations of manual, fiducial and surface-based registration
 *'''Slicer 3.6.1 recommended modules:
-** [http://www.slicer.org/slicerWiki/index.php/Modules:PythonSurfaceICPRegistration-Documentation-3.6 Surface Registration]
+** [https://www.slicer.org/wiki/Modules:PythonSurfaceICPRegistration-Documentation-3.6 Surface Registration]
-** [http://www.slicer.org/slicerWiki/index.php/Modules:Plastimatch Plastimatch]
+** [https://www.slicer.org/wiki/Modules:Plastimatch Plastimatch]
 === Registration Results===

@@ Line 23: / Line 23: @@
 *DATA
 **[[Media:RegLib_C35_Data.zip‎|'''Registration Library Case 35 '''<small> (Data,  zip file 46 MB) </small>]]
 === Keywords ===

@@ Line 46: / Line 46: @@
 === Registration Results===
 [[Image:RegLibC35_Models.png |200px| very rough surface models of colon help visualize misalignment]] very rough surface models of colon help visualize misalignment<br>
-[[Image:RegLibC35_unreg.gif‎ |500px|original unregistered]] original, not registered<br>
+[[Image:RegLibC35_unreg.gif‎ |200px|original unregistered]] original, not registered<br>
-[[Image:RegLibC35_reg.gif |500px| after surface registration (rigid) + manual correction]] after surface registration (rigid) + manual correction<br>
+[[Image:RegLibC35_reg.gif |200px| after surface registration (rigid) + manual correction]] after surface registration (rigid) + manual correction<br>
 <br>

@@ Line 6: / Line 6: @@
 === Input ===
 {| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
-|[[Image:RegLib_C35_Thumb1.png|150px|lleft|case A]]
+|[[Image:RegLibC35_Thumb1.png|150px|lleft|case A]]
 |[[Image:RegArrow_NonRigid.png|100px|lleft]]
-|[[Image:RegLib_C35_Thumb2.png|150px|lleft|case B]]
+|[[Image:RegLibC35_Thumb2.png|150px|lleft|case B]]
 |-
 |fixed image 1/target<br>MRI mouse 1
@@ Line 45: / Line 45: @@
 === Registration Results===
-[[Image:RegLib_C35_Models.png |200px| very rough surface models of colon help visualize misalignment]] very rough surface models of colon help visualize misalignment<br>
+[[Image:RegLibC35_Models.png |200px| very rough surface models of colon help visualize misalignment]] very rough surface models of colon help visualize misalignment<br>
-[[Image:RegLib_C35_unreg.gif‎ |500px|original unregistered]] original, not registered<br>
+[[Image:RegLibC35_unreg.gif‎ |500px|original unregistered]] original, not registered<br>
-[[Image:RegLib_C35_reg.gif |500px| after surface registration (rigid) + manual correction]] after surface registration (rigid) + manual correction<br>
+[[Image:RegLibC35_reg.gif |500px| after surface registration (rigid) + manual correction]] after surface registration (rigid) + manual correction<br>
 <br>

@@ Line 45: / Line 45: @@
 === Registration Results===
-[[Image:RegLib_C35_Model.png |200px| very rough surface models of colon help visualize misalignment] very rough surface models of colon help visualize misalignment<br>
+[[Image:RegLib_C35_Models.png |200px| very rough surface models of colon help visualize misalignment]] very rough surface models of colon help visualize misalignment<br>
 [[Image:RegLib_C35_unreg.gif‎ |500px|original unregistered]] original, not registered<br>
 [[Image:RegLib_C35_reg.gif |500px| after surface registration (rigid) + manual correction]] after surface registration (rigid) + manual correction<br>
 <br>

@@ Line 34: / Line 34: @@
 ===Registration Challenges===
 *The image content to be registered is less than 10% of the total image and of low energy (close to background);
-[[Image:RegLibC35_Histogram.png|150px|lleft|histogram of image content: target structure (colon, red) is very small amount of total image energy, making intensity-based automated approach unlikely to succeed]]
+[[Image:RegLib_C35_Histogram.png|150px|lleft|histogram of image content: target structure (colon, red) is very small amount of total image energy, making intensity-based automated approach unlikely to succeed]]
 *there's large portions of the colon for which no matching/corresponding structures exist, i.e. a straightforward one-one mapping is not avail.
 *other landmarks (kidneys etc.) are very different in position and size